Providing you haven't changed your location for saving to somewhere unsafe (eg within LW's program files) then your saved downloads should be fine

You can check in LW's tools > options > saving. The default location for saving is C:\Documents and Settings\your username\Shared.

If you're going to reinstall LW, you can install over the top of the existing version...installing a new LW will automatically remove the old one. Don't uninstall via Add/Remove Programs...that can cause problems. If you do want to uninstall the old LW first, do it via Start > All Programs > Limewire > use the uninstall option there